A new method is proposed called gene expression tomography, or GET, that will increase the speed of 3D gene expression analysis in the brain. The name is evocative of the method's dual foundations in high throughput gene expression analysis and computerized tomographic image reconstruction familiar from biomedical imaging. The technique involves taking brain slices using a cryostat in conjunction with axial rotation about orthogonal axes to create a series of "view" of the brain. mRNA is extracted from the slices and gene expression levels can then be analyzed using any high throughput technique. Real-time quantitative RT-PCR is employed in this proposal, because of its sensitivity, robustness and simplicity. The gene expression information obtained from the axially rotated views can then be used in image reconstruction algorithms to recreate the 3D gene expression pattern within the brain. In essence, the method transforms the complex 3D anatomy of the brain into 2D tissue slices, which are further simplified into 1D arrays of zero dimensional (0D) biochemical samples. The 1D arrays amenable to high throughput analysis with attendant advantages of scalability and automatability, allowing greatly increased speed of 3D gene expression analysis. Unlike in situ hybridization, which requires a new brain for analysis of each gene, the technique proposed here needs only a limited number of brains for analysis of a large number of genes. The method can in principle be used to document the expression patterns of all genes within the brain and can thus allow the characteristic "fingerprint" or "signature" of gene expression in time and space of a particular brain region to be identified. This should give important insights into brain development. In addition, the method can be used to discern the mutually interdependent regulation of gene networks in response to environmental and genetic perturbations, allowing improved understanding of brain disorders and suggesting new therapies. This proposal concentrates on the mouse, because of its well-established genome project and the simple access to mouse brains. However, other organisms could be employed and the technique could be used with great profit to study the rat or human brain. The long-terms goal is to obtain the expression patterns of all genes in the brain. This will enable decoding of the genetic circuitry of the brain in health and disease, and rational design of new therapies.